#!/usr/bin/env Rscript             
#########################################################
# TASK: formatting data that will be used for various plots

# useful links
#https://stackoverflow.com/questions/38851592/r-append-column-in-a-dataframe-with-frequency-count-based-on-two-columns
#########################################################
# working dir and loading libraries
getwd()
setwd("~/git/LSHTM_analysis/scripts/plotting")
getwd()

#source("Header_TT.R")
require("getopt", quietly = TRUE) #cmd parse arguments
#========================================================
# command line args
#spec = matrix(c(
#  "drug"   , "d", 1, "character",
#  "gene"   , "g", 1, "character"
#), byrow = TRUE, ncol = 4)

#opt = getopt(spec)

#drug = opt$druggene = opt$gene

#if(is.null(drug)|is.null(gene)) {
#  stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
#}
#========================================================
#%% variable assignment: input and output paths & filenames
drug = "pyrazinamide"
gene = "pncA"
gene_match = paste0(gene,"_p.")
cat(gene_match)

#=============
# directories
#=============
datadir = paste0("~/git/Data")
indir = paste0(datadir, "/", drug, "/input")
outdir = paste0("~/git/Data", "/", drug, "/output")

#======
# input
#======
#in_filename = "mcsm_complex1_normalised.csv"
in_filename_params = paste0(tolower(gene), "_all_params.csv") 
infile_params = paste0(outdir, "/", in_filename_params)
cat(paste0("Input file 1:", infile_params) )

#%%===============================================================
###########################
# Read file: struct params
###########################
cat("Reading struct params including mcsm:", in_filename_params)
    
my_df = read.csv(infile_params, header = T)

cat("Input dimensions:", dim(my_df)) 

# quick checks
#colnames(my_df)
#str(my_df)

# check for duplicate mutations
if ( length(unique(my_df$mutationinformation)) != length(my_df$mutationinformation)){
  cat(paste0("CAUTION:", " Duplicate mutations identified"
             , "\nExtracting these..."))
  dup_muts = my_df[duplicated(my_df$mutationinformation),]
  dup_muts_nu = length(unique(dup_muts$mutationinformation))
  cat(paste0("\nDim of duplicate mutation df:", nrow(dup_muts)
             , "\nNo. of unique duplicate mutations:", dup_muts_nu
             , "\n\nExtracting df with unique mutations only"))
  my_df_u = my_df[!duplicated(my_df$mutationinformation),]
}else{
  cat(paste0("No duplicate mutations detected"))
  my_df_u = my_df
}

upos = unique(my_df_u$position)
cat("Dim of clean df:"); cat(dim(my_df_u))
cat("\nNo. of unique mutational positions:"); cat(length(upos), "\n")
  
########################################################################
#               end of data extraction and cleaning for plots          #
########################################################################
# clear variables
rm(opt, spec)